\chapter{Common Errors}

\section{Errors while reading input file}
Our file reader catches some errors, like files not exisiting or
being unable to open them. Look at the verbose stream of the
program to make sure all your flags are being caught, and check the
stream for errors as well.

\section{Segmentation Fault while reading input file}
Our file reader is not very robust.
Make sure there is only a single space between keywords and options.
Make sure that all options are specified for a given keyword.

\section{Initial configuration errors}
Many issues may arise if your molecules are overlapping, which is not allowed in the PB solvers' models.
The center of the molecule will be placed at the positions given by each XYZ file.
Check the printed out PQR file for the initial configuration, which you can load into VMD.
Try changing the xyz file(s).
This error may also appear if the box length specified with the pbc keyword is too small.
Try increasing the box length.










